You can try two things:
Option 1:
- Copy the files to a path under “private/files” folder of the site using SFTP or any other file protocol.
- Create a “File” Doctype record with necessary attributes through a scheduled job in Frappe or directly from Windows using curl.
Option 2:
Option 1 or 2 will be based on the number of files that you need to process. If there are 100s of files, my preference will be to use Option 1.